JAL-2431 show cDNA consensus after New View in split frame

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 921429b..f7a1d2c 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -25,7 +25,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -297,7 +297,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Highlight the given results on the alignment.
    * 
    */
-  public void highlightSearchResults(SearchResults results)
+  public void highlightSearchResults(SearchResultsI results)
   {
     scrollToPosition(results);
     getSeqPanel().seqCanvas.highlightSearchResults(results);
@@ -309,7 +309,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @param results
    */
-  public boolean scrollToPosition(SearchResults results)
+  public boolean scrollToPosition(SearchResultsI results)
   {
     return scrollToPosition(results, 0, true, false);
   }
@@ -322,7 +322,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param redrawOverview
    * @return
    */
-  public boolean scrollToPosition(SearchResults searchResults,
+  public boolean scrollToPosition(SearchResultsI searchResults,
           boolean redrawOverview)
   {
     return scrollToPosition(searchResults, 0, redrawOverview, false);
@@ -342,7 +342,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          if true, try to centre the search results horizontally in the view
    * @return false if results were not found
    */
-  public boolean scrollToPosition(SearchResults results,
+  public boolean scrollToPosition(SearchResultsI results,
           int verticalOffset, boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
@@ -1299,8 +1299,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (onscreen
             || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
     {
-      return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
-              : calculateIdWidth().width + 4);
+      int w = getIdPanel().getWidth();
+      return (w > 0 ? w : calculateIdWidth().width + 4);
     }
     return idwidth.intValue() + 4;
   }
@@ -1448,7 +1448,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
-    // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+    // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
     // ////////////////////////////////////////////
     int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
@@ -1462,7 +1462,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
                 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
-        StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
         out.println(jalview.io.HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName
@@ -1478,7 +1477,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
-            text = new StringBuffer();
+            StringBuilder text = new StringBuilder();
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
@@ -1502,18 +1501,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
             {
               if (text.length() < 1)
               {
-                text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.getCharWidth()) + "," + sy
-                        + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + "," + (av.getCharHeight() + sy) + "\""
-                        + " onMouseOver=\"toolTip('" + alIndex + " "
-                        + triplet);
+                text.append("<area shape=\"rect\" coords=\"")
+                        .append((idWidth + res * av.getCharWidth()))
+                        .append(",").append(sy).append(",")
+                        .append((idWidth + (res + 1) * av.getCharWidth()))
+                        .append(",").append((av.getCharHeight() + sy))
+                        .append("\"").append(" onMouseOver=\"toolTip('")
+                        .append(alIndex).append(" ").append(triplet);
               }
 
               if (groups[g].getStartRes() < res
                       && groups[g].getEndRes() > res)
               {
-                text.append("<br><em>" + groups[g].getName() + "</em>");
+                text.append("<br><em>").append(groups[g].getName())
+                        .append("</em>");
               }
             }
 
@@ -1521,12 +1522,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
             {
               if (text.length() < 1)
               {
-                text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.getCharWidth()) + "," + sy
-                        + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + "," + (av.getCharHeight() + sy) + "\""
-                        + " onMouseOver=\"toolTip('" + alIndex + " "
-                        + triplet);
+                text.append("<area shape=\"rect\" coords=\"")
+                        .append((idWidth + res * av.getCharWidth()))
+                        .append(",").append(sy).append(",")
+                        .append((idWidth + (res + 1) * av.getCharWidth()))
+                        .append(",").append((av.getCharHeight() + sy))
+                        .append("\"").append(" onMouseOver=\"toolTip('")
+                        .append(alIndex).append(" ").append(triplet);
               }
               fSize = features.length;
               for (f = 0; f < fSize; f++)
@@ -1535,15 +1537,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 if ((features[f].getBegin() <= seq.findPosition(res))
                         && (features[f].getEnd() >= seq.findPosition(res)))
                 {
-                  if (features[f].getType().equals("disulfide bond"))
+                  if (features[f].isContactFeature())
                   {
                     if (features[f].getBegin() == seq.findPosition(res)
                             || features[f].getEnd() == seq
                                     .findPosition(res))
                     {
-                      text.append("<br>disulfide bond "
-                              + features[f].getBegin() + ":"
-                              + features[f].getEnd());
+                      text.append("<br>").append(features[f].getType())
+                              .append(" ").append(features[f].getBegin())
+                              .append(":").append(features[f].getEnd());
                     }
                   }
                   else
@@ -1554,13 +1556,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
                             && !features[f].getType().equals(
                                     features[f].getDescription()))
                     {
-                      text.append(" " + features[f].getDescription());
+                      text.append(" ").append(features[f].getDescription());
                     }
 
                     if (features[f].getValue("status") != null)
                     {
-                      text.append(" (" + features[f].getValue("status")
-                              + ")");
+                      text.append(" (").append(features[f].getValue("status"))
+                              .append(")");
                     }
                   }
                 }
@@ -1825,14 +1827,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param verticalOffset
    *          the number of visible sequences to show above the mapped region
    */
-  public void scrollToCentre(SearchResults sr, int verticalOffset)
+  public void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
     /*
      * To avoid jumpy vertical scrolling (if some sequences are gapped or not
      * mapped), we can make the scroll-to location a sequence above the one
      * actually mapped.
      */
-    SequenceI mappedTo = sr.getResultSequence(0);
+    SequenceI mappedTo = sr.getResults().get(0).getSequence();
     List<SequenceI> seqs = av.getAlignment().getSequences();
 
     /*
@@ -1873,4 +1875,26 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return this.dontScrollComplement;
   }
+
+  /**
+   * Redraw sensibly.
+   * 
+   * @adjustHeight if true, try to recalculate panel height for visible
+   *               annotations
+   */
+  protected void refresh(boolean adjustHeight)
+  {
+    validateAnnotationDimensions(adjustHeight);
+    addNotify();
+    if (adjustHeight)
+    {
+      // sort, repaint, update overview
+      paintAlignment(true);
+    }
+    else
+    {
+      // lightweight repaint
+      repaint();
+    }
+  }
 }